SMTL ID : 2bgm.1

X-Ray structure of ternary-Secoisolariciresinol Dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NAJ: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)(Non-covalent)

NAJ.1: 24 residues within 4Å: Chain A: G.23, G.26, G.27, I.28, D.47, I.48, C.71, D.72, V.73, N.99, V.100, G.101, V.102, I.124, T.151, A.152, S.153, Y.167, K.171, P.197, Y.198, I.199, V.200 Ligands: MAX.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.27, A:I.28, A:I.48, A:D.72, A:V.73, A:N.99, A:Y.167, A:K.171, A:V.200, A:V.200 Water bridges: A:G.26, A:G.29 NAJ.3: 24 residues within 4Å: Chain B: G.23, G.26, G.27, I.28, D.47, I.48, C.71, D.72, V.73, N.99, V.100, G.101, V.102, I.124, T.151, A.152, S.153, Y.167, K.171, P.197, Y.198, I.199, V.200 Ligands: MAX.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.27, B:I.28, B:I.48, B:D.72, B:V.73, B:N.99, B:K.171, B:V.200, B:V.200 Water bridges: B:G.26, B:N.99 NAJ.5: 24 residues within 4Å: Chain C: G.23, G.26, G.27, I.28, D.47, I.48, C.71, D.72, V.73, N.99, V.100, G.101, V.102, I.124, T.151, A.152, S.153, Y.167, K.171, P.197, Y.198, I.199, V.200 Ligands: MAX.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.27, C:I.28, C:I.48, C:D.72, C:V.73, C:N.99, C:K.171, C:V.200, C:V.200 Water bridges: C:G.26, C:N.99 NAJ.7: 24 residues within 4Å: Chain D: G.23, G.26, G.27, I.28, D.47, I.48, C.71, D.72, V.73, N.99, V.100, G.101, V.102, I.124, T.151, A.152, S.153, Y.167, K.171, P.197, Y.198, I.199, V.200 Ligands: MAX.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.27, D:I.28, D:I.48, D:D.72, D:V.73, D:N.99, D:Y.167, D:K.171, D:V.200, D:V.200 Water bridges: D:G.26, D:G.29

4 x MAX: MATAIRESINOL(Non-covalent)

MAX.2: 14 residues within 4Å: Chain A: L.103, S.104, S.153, I.154, G.162, V.163, S.164, Y.167, P.197, Y.198, I.199, Y.262 Chain B: F.269 Ligands: NAJ.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.103, A:V.163, A:I.199, B:F.269 Hydrogen bonds: A:S.104, A:S.164 MAX.4: 14 residues within 4Å: Chain A: F.269 Chain B: L.103, S.104, S.153, I.154, G.162, V.163, S.164, Y.167, P.197, Y.198, I.199, Y.262 Ligands: NAJ.3 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.103, B:V.163, B:I.199, A:F.269 Hydrogen bonds: B:S.104, B:S.164 Water bridges: B:Y.262 MAX.6: 14 residues within 4Å: Chain C: L.103, S.104, S.153, I.154, G.162, V.163, S.164, Y.167, P.197, Y.198, I.199, Y.262 Chain D: F.269 Ligands: NAJ.5 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.103, C:V.163, C:I.199, D:F.269 Hydrogen bonds: C:S.104, C:S.164 Water bridges: C:Y.262 MAX.8: 14 residues within 4Å: Chain C: F.269 Chain D: L.103, S.104, S.153, I.154, G.162, V.163, S.164, Y.167, P.197, Y.198, I.199, Y.262 Ligands: NAJ.7 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.103, D:V.163, D:I.199, C:F.269 Hydrogen bonds: D:S.104, D:S.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Youn, B. et al., Crystal Structures of Apo-Form and Binary/Ternary Complexes of Podophyllum Secoisolariciresinol Dehydrogenase, an Enzyme Involved in Formation of Health-Protecting and Plant Defense Lignans. J.Biol.Chem. (2005)

Release Date

2005-01-13

Peptides

RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE

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